perf(link_z): derive big-M from variable bounds instead of a per-row LP - #69

Merged

VonAlphaBisZulu merged 56 commits into

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perf-remove-boundm-lp-main

Jul 25, 2026

Commits on Jul 13, 2026

perf(link_z): derive big-M from variable bounds instead of a per-row LP

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f58f9d6
Merge branch 'main' into perf-remove-boundm-lp-main
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87fdbb0

Commits on Jul 17, 2026

docs(link_z): note the arity-1 bound-fold consolidation step (not enabled)

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bc81541
perf(reassign_lb_ub_from_ineq): linear arity scan instead of O(nnz^2)

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283c9b4
perf(link_z): fix structurally-vacuous intervention binaries to zero

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a130ce7
feat(protect): per-block region-FVA bounds (blocked + reversibility), opt-in

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66a9f83
feat(protect): make region-FVA unconditional (remove protect_region_fva switch)

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1c22d63
feat(compression): revert compression-induced coeff shift in module constraints

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ff2ac5a
refactor(fva): compute region FVA once for all modules; SDMILP reads stored bounds

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9cb4482
feat(protect->suppress): apply region-FVA bound override to SUPPRESS too

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477b152
refactor(link_z): fix free intervention binaries at END of link_z (was: start)

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33f8592

Commits on Jul 18, 2026

Commits on Jul 19, 2026

perf(enum): add k-sweep enumeration loop; default it for CPLEX (~2x, near gMCSpy parity)

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1b2ae8d

Commits on Jul 20, 2026

Commits on Jul 21, 2026

perf(compress): pre-tighten reaction reversibility before compress #1

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feat(gpr): monotone GPR-rule minimizer to shrink the gadget in gene-based MCS

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78f144d

Commits on Jul 22, 2026

perf(SDProblem): drop solver/optlang + FVA deps in construction; fix O(n^2) in link_z

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287f9da
fix(compression): make compress_model_coupled stub-solver safe

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5cd9a1e
fix(enum): guard k-sweep against non-integer intervention costs

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e96072f
change(enum): stop defaulting CPLEX to k-sweep; use populate for all solvers

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df775fb
style(comments): describe usage and intent, not change history

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3e5af6c
refactor(compression): prune stale groups in suppress_lp_context; drop sympy from GPR merging

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test(gpr): cover the ast-based GPR helpers; use cobra as_symbolic for equivalence

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Merge main into perf-remove-boundm-lp-main (draft-PR CI skip)
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cb0cdeb
refactor(compression): one GPR-combine entry point; inline stale-group pruning

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f70a11f
chore: untrack perf-test result artefacts

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b7e43fe
refactor: disable the k-sweep enumeration path; fold the cheap model copy into suppress_lp_context

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d6a9136
fix(compression): keep lumped reactions in their most-detailed member's scale

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f73f262

Commits on Jul 23, 2026

fix(compression): prefer preserving a small finite bound when rescaling a lump

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cad2994
refactor(gpr): rename gpr_bitmask -> gpr_simplify, to_cover -> to_dnf

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e1f94d3
docs/naming: address PR #69 review comments (comments, docstrings, to_fraction renames)

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bcfffb0
docs: update renamed symbol references to *_to_fraction in developers guide

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762b47d
refactor(compression): co-locate nnz and small-bound scale-member choice

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6558f45
refactor(gpr): run simplify before gpr count log + report elapsed time

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0b44192
test(preprocessing): group per-case GPR helper tests via parametrize

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e23dc79

Commits on Jul 24, 2026

refactor(speedy_fva): hoist degeneracy-guard tolerance to _DEGEN_TOL

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971d2d9
perf(suppress): drop live solver backend from suppressed model copies

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refactor(override): _region_fva_override -> _region_bound_override (general module bound override)

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refactor(override): _region_bound_override -> _module_bound_override, drop alias

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62e0af2
refactor(gpr): move GPR simplification into compression.py + run it in compress_model

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refactor(gpr): move reduce_gpr -> reduce_model_gprs into the pipeline file

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refactor(gpr): (b) reduce_model_gprs delegates boolean simplification to simplify_model_gprs

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639a8e8
perf(preprocessing): fold single-module FVA passes
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style(compression): simplify section comments
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docs(guide): rewrite developer's guide for the current pipeline

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0d1f170
fix(reversibility): decide directions on exact signs, never on an unsolved bound

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5642a24
fix(override): require a real margin before fixing a module bound on SCIP/GLPK

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3f90de7
fix(compression): compare backends up to lump scale, warn on efmtool_rref

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9c1b890
refactor(preprocessing): give the module essentiality rule a single home

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fix(preprocessing): lift the essentiality margin above solver feasibility tolerance

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219305b
docs(guide): cite code by symbol, and correct claims that contradict the source

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